xml update

generate a bigwig (bw) file from a bed (remove non-nuclear genomes first)

for i in ./*bed; do perl -wnl -e ‘/Chr\d/ and print;’ $i | bedtools genomecov -bg -i – -g ~/bsgenome_tair9.Chr.txt > ${i%%bed}bg; done


for i in ./*bg; do bedGraphToBigWig $i ~/bsgenome_tair9.Chr.txt ${i%%bg}bw; done

collect the names of these bw

ls -l | awk ‘{print $9}’ | grep bw > file_names.txt

perl -wpl -e ‘s|^(.*)$|<Resource name=”$1″ path=”http://yourServerHere/igvdata/chip_seq_jic/$1″/>|g;’ file_names.txt > xml.tmp

paste names from this new file into the field of a new igvdata xml with appropriately descriptive global and category headers,

add this xml to your igv_registry.txt in your /var/www/html/igv directory,
and import the bw files to an appropriately named directory in /var/www/html/igvdata

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